Journal article

Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing

James R Knight, Eileen M Dunne, E Kim Mulholland, Sudipta Saha, Catherine Satzke, Adrienn Tothpal, Daniel M Weinberger



Serotyping of Streptococcus pneumoniae is a critical tool in the surveillance of the pathogen and in the development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software requires samples to be pure (or nearly pure) and only contain a single pneumococcal serotype. We introduce a new software tool called SeroCall, which can identify and quantitate the serotypes present in samples, even when several serotypes are present. The sample preparation, library preparation a..

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Awarded by NIH/NIAID

Awarded by NHMRC Career Development Fellowship

Awarded by PneumoCarr Consortium

Awarded by Bill and Melinda Gates Foundation

Funding Acknowledgements

This work was funded by a grant from NIH/NIAID to D. M. W. (R01AI123208,R56AI110449). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. C. S. was supported by a NHMRC Career Development Fellowship (1087957) and a veski Inspiring Women Fellowship. This project was also supported by the Victorian Government's Operational Infrastructure Support Programme. The PneuCarriage samples were prepared under a grant funded through the PneumoCarr Consortium (grant 37875) and the Bill and Melinda Gates Foundation (grant 52099).